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dsr2xml(1)			  OFFIS	DCMTK			    dsr2xml(1)

NAME
       dsr2xml - Convert DICOM SR file and data	set to XML

SYNOPSIS
       dsr2xml [options] dsrfile-in [xmlfile-out]

DESCRIPTION
       The  dsr2xml  utility  converts	the  contents  of  a  DICOM Structured
       Reporting  (SR)	document  (file	 format	 or  raw  data	set)  to   XML
       (Extensible  Markup  Language). The XML Schema dsr2xml.xsd does not yet
       follow any standard format. However, the	dsr2xml	application  might  be
       enhanced	 in  this  aspect  in the future (e.g. by supporting HL7/CDA -
       Clinical	Document Architecture).

       If dsr2xml reads	a raw data set (DICOM data without a file format meta-
       header) it will attempt to guess	the transfer syntax by	examining  the
       first  few  bytes  of  the file.	It is not always possible to correctly
       guess the transfer syntax and it	is better to convert a data set	 to  a
       file  format  whenever possible (using the dcmconv utility). It is also
       possible	to use the -f and -t[ieb] options to force dsr2xml to  read  a
       dataset with a particular transfer syntax.

PARAMETERS
       dsrfile-in   DICOM SR input filename to be converted ("-" for stdin)

       xmlfile-out  XML	output filename	(default: stdout)

OPTIONS
   general options
	 -h   --help
		print this help	text and exit

	      --version
		print version information and exit

	      --arguments
		print expanded command line arguments

	 -q   --quiet
		quiet mode, print no warnings and errors

	 -v   --verbose
		verbose	mode, print processing details

	 -d   --debug
		debug mode, print debug	information

	 -ll  --log-level  [l]evel: string constant
		(fatal,	error, warn, info, debug, trace)
		use level l for	the logger

	 -lc  --log-config  [f]ilename:	string
		use config file	f for the logger

   input options
       input file format:

	 +f   --read-file
		read file format or data set (default)

	 +fo  --read-file-only
		read file format only

	 -f   --read-dataset
		read data set without file meta	information

       input transfer syntax:

	 -t=  --read-xfer-auto
		use TS recognition (default)

	 -td  --read-xfer-detect
		ignore TS specified in the file	meta header

	 -te  --read-xfer-little
		read with explicit VR little endian TS

	 -tb  --read-xfer-big
		read with explicit VR big endian TS

	 -ti  --read-xfer-implicit
		read with implicit VR little endian TS

   processing options
       error handling:

	 -Er  --unknown-relationship
		accept unknown/missing relationship type

	 -Ev  --invalid-item-value
		accept invalid content item value
		(e.g. violation	of VR or VM definition)

	 -Ec  --ignore-constraints
		ignore relationship content constraints

	 -Ee  --ignore-item-errors
		do not abort on	content	item errors, just warn
		(e.g. missing value type specific attributes)

	 -Ei  --skip-invalid-items
		skip invalid content items (including sub-tree)

	 -Dv  --disable-vr-checker
		disable	check for VR-conformant	string values

       specific	character set:

	 +Cr  --charset-require
		require	declaration of extended	charset	(default)

	 +Ca  --charset-assume	[c]harset: string
		assume charset c if no extended	charset	declared

	 +Cc  --charset-check-all
		check all data elements	with string values
		(default: only PN, LO, LT, SH, ST, UC and UT)

		# this option is only used for the extended check whether
		# the Specific Character Set (0008,0005) attribute should be
		# present, but not for the conversion of unaffected element
		# values to UTF-8 (e.g.	element	values with a VR of CS)

	 +U8  --convert-to-utf8
		convert	all element values that	are affected
		by Specific Character Set (0008,0005) to UTF-8

		# requires support from	an underlying character	encoding
		# library (see output of --version on which one	is available)

   output options
       encoding:

	 +Ea  --attr-all
		encode everything as XML attribute
		(shortcut for +Ec, +Er,	+Ev and	+Et)

	 +Ec  --attr-code
		encode code value, coding scheme designator
		and coding scheme version as XML attribute

	 +Er  --attr-relationship
		encode relationship type as XML	attribute

	 +Ev  --attr-value-type
		encode value type as XML attribute

	 +Et  --attr-template-id
		encode template	id as XML attribute

	 +Ee  --template-envelope
		template element encloses content items
		(requires +Wt, implies +Et)

       XML structure:

	 +Xs  --add-schema-reference
		add reference to XML Schema "dsr2xml.xsd"
		(not with +Ea, +Ec, +Er, +Ev, +Et, +Ee,	+We)

	 +Xn  --use-xml-namespace
		add XML	namespace declaration to root element

       writing:

	 +We  --write-empty-tags
		write all tags even if their value is empty

	 +Wi  --write-item-id
		always write item identifier

	 +Wt  --write-template-id
		write template identification information

NOTES
   DICOM Conformance
       The dsr2xml utility supports the	following SOP Classes:

       SpectaclePrescriptionReportStorage	    1.2.840.10008.5.1.4.1.1.78.6
       MacularGridThicknessAndVolumeReportStorage   1.2.840.10008.5.1.4.1.1.79.1
       BasicTextSRStorage			    1.2.840.10008.5.1.4.1.1.88.11
       EnhancedSRStorage			    1.2.840.10008.5.1.4.1.1.88.22
       ComprehensiveSRStorage			    1.2.840.10008.5.1.4.1.1.88.33
       Comprehensive3DSRStorage			    1.2.840.10008.5.1.4.1.1.88.34
       ProcedureLogStorage			    1.2.840.10008.5.1.4.1.1.88.40
       MammographyCADSRStorage			    1.2.840.10008.5.1.4.1.1.88.50
       KeyObjectSelectionDocumentStorage	    1.2.840.10008.5.1.4.1.1.88.59
       ChestCADSRStorage			    1.2.840.10008.5.1.4.1.1.88.65
       XRayRadiationDoseSRStorage		    1.2.840.10008.5.1.4.1.1.88.67
       RadiopharmaceuticalRadiationDoseSRStorage    1.2.840.10008.5.1.4.1.1.88.68
       ColonCADSRStorage			    1.2.840.10008.5.1.4.1.1.88.69
       ImplantationPlanSRStorage		    1.2.840.10008.5.1.4.1.1.88.70
       AcquisitionContextSRStorage		    1.2.840.10008.5.1.4.1.1.88.71
       SimplifiedAdultEchoSRStorage		    1.2.840.10008.5.1.4.1.1.88.72
       PatientRadiationDoseSRStorage		    1.2.840.10008.5.1.4.1.1.88.73
       PlannedImagingAgentAdministrationSRStorage   1.2.840.10008.5.1.4.1.1.88.74
       PerformedImagingAgentAdministrationSRStorage 1.2.840.10008.5.1.4.1.1.88.75
       WaveformAnnotationSRStorage		    1.2.840.10008.5.1.4.1.1.88.77

       Please  note that currently only	mandatory and some optional attributes
       are supported.

   Character Encoding
       The XML encoding	is determined automatically from the  DICOM  attribute
       (0008,0005) 'Specific Character Set' using the following	mapping:

       ASCII	     (ISO_IR 6)			      =>  "UTF-8"
       UTF-8	     "ISO_IR 192"		      =>  "UTF-8"
       ISO Latin 1   "ISO_IR 100"		      =>  "ISO-8859-1"
       ISO Latin 2   "ISO_IR 101"		      =>  "ISO-8859-2"
       ISO Latin 3   "ISO_IR 109"		      =>  "ISO-8859-3"
       ISO Latin 4   "ISO_IR 110"		      =>  "ISO-8859-4"
       ISO Latin 5   "ISO_IR 148"		      =>  "ISO-8859-9"
       ISO Latin 9   "ISO_IR 203"		      =>  "ISO-8859-15"
       Cyrillic	     "ISO_IR 144"		      =>  "ISO-8859-5"
       Arabic	     "ISO_IR 127"		      =>  "ISO-8859-6"
       Greek	     "ISO_IR 126"		      =>  "ISO-8859-7"
       Hebrew	     "ISO_IR 138"		      =>  "ISO-8859-8"
       Thai	     "ISO_IR 166"		      =>  "TIS-620"
       Japanese	     "ISO 2022 IR 13ISO	2022 IR	87"  =>	 "ISO-2022-JP"
       Korean	     "ISO 2022 IR 6ISO 2022 IR 149"  =>	 "ISO-2022-KR"
       Chinese	     "ISO 2022 IR 6ISO 2022 IR 58"   =>	 "ISO-2022-CN"
       Chinese	     "GB18030"			      =>  "GB18030"
       Chinese	     "GBK"			      =>  "GBK"

       If  this	DICOM attribute	is missing in the input	file, although needed,
       option --charset-assume can be used to specify an appropriate character
       set manually (using one of the DICOM defined  terms).  For  reasons  of
       backward	 compatibility	with  previous	versions  of  this  tool,  the
       following terms are also	supported  and	mapped	automatically  to  the
       associated  DICOM  defined  terms:  latin-1, latin-2, latin-3, latin-4,
       latin-5,	latin-9, cyrillic, arabic, greek, hebrew.

       Option --convert-to-utf8	can be used to convert the DICOM file or  data
       set to UTF-8 encoding prior to the conversion to	XML format.

       If no mapping is	defined	and option --convert-to-utf8 is	not used, non-
       ASCII characters	and those below	#32 are	stored as '&#nnn;' where 'nnn'
       refers  to  the	numeric	 character  code.  This	 might lead to invalid
       character entity	references (such as '' for	ESC)  and  will	 cause
       most XML	parsers	to reject the document.

   Error Handling
       Please  be  careful with	the processing options --unknown-relationship,
       --invalid-item-value,  --ignore-constraints,  --ignore-item-errors  and
       --skip-invalid-items  since  they  disable certain validation checks on
       the DICOM SR input file and, therefore, might  result  in  non-standard
       conformant  output.  However,  there  might be reasons for using	one or
       more of these options, e.g. in order to read and	process	an incorrectly
       encoded SR document.

   Limitations
       The XML Schema dsr2xml.xsd does	not  support  all  variations  of  the
       dsr2xml	output format. However,	the default output format (plus	option
       --use-xml-namespace) should work.

LOGGING
       The level of logging output of  the  various  command  line  tools  and
       underlying  libraries  can  be  specified by the	user. By default, only
       errors and warnings are written to the  standard	 error	stream.	 Using
       option  --verbose  also	informational messages like processing details
       are reported. Option --debug can	be used	to get	more  details  on  the
       internal	 activity,  e.g.  for debugging	purposes. Other	logging	levels
       can be selected using option --log-level. In --quiet  mode  only	 fatal
       errors  are reported. In	such very severe error events, the application
       will usually terminate. For  more  details  on  the  different  logging
       levels, see documentation of module 'oflog'.

       In  case	 the logging output should be written to file (optionally with
       logfile rotation), to syslog (Unix) or the event	log  (Windows)	option
       --log-config  can  be  used.  This  configuration  file also allows for
       directing only certain messages to a particular output stream  and  for
       filtering  certain  messages  based  on the module or application where
       they are	generated.  An	example	 configuration	file  is  provided  in
       <etcdir>/logger.cfg.

COMMAND	LINE
       All  command  line  tools  use  the  following notation for parameters:
       square brackets enclose optional	 values	 (0-1),	 three	trailing  dots
       indicate	 that multiple values are allowed (1-n), a combination of both
       means 0 to n values.

       Command line options are	distinguished from parameters by a leading '+'
       or '-' sign, respectively. Usually, order and position of command  line
       options	are  arbitrary	(i.e.  they  can appear	anywhere). However, if
       options are mutually exclusive the rightmost appearance is  used.  This
       behavior	 conforms  to  the  standard  evaluation  rules	of common Unix
       shells.

       In addition, one	or more	command	files can be specified	using  an  '@'
       sign  as	 a  prefix to the filename (e.g. @command.txt).	Such a command
       argument	is replaced by the content  of	the  corresponding  text  file
       (multiple  whitespaces  are  treated  as	a single separator unless they
       appear between two quotation marks) prior to  any  further  evaluation.
       Please  note  that  a command file cannot contain another command file.
       This simple but effective  approach  allows  one	 to  summarize	common
       combinations  of	 options/parameters  and  avoids longish and confusing
       command lines (an example is provided in	file <datadir>/dumppat.txt).

ENVIRONMENT
       The dsr2xml utility  will  attempt  to  load  DICOM  data  dictionaries
       specified  in the DCMDICTPATH environment variable. By default, i.e. if
       the  DCMDICTPATH	 environment   variable	  is   not   set,   the	  file
       <datadir>/dicom.dic  will be loaded unless the dictionary is built into
       the application (default	for Windows).

       The  default  behavior  should  be  preferred   and   the   DCMDICTPATH
       environment  variable  only used	when alternative data dictionaries are
       required. The DCMDICTPATH environment variable has the same  format  as
       the  Unix  shell	PATH variable in that a	colon (':') separates entries.
       On Windows systems, a semicolon (';') is	used as	a separator. The  data
       dictionary  code	 will  attempt	to  load  each	file  specified	in the
       DCMDICTPATH environment variable. It is an error	if no data  dictionary
       can be loaded.

       Depending  on  the  command line	options	specified, the dsr2xml utility
       will attempt to load character set mapping tables.  This	 happens  when
       DCMTK  was compiled with	the oficonv library (which is the default) and
       the mapping tables are not built	into the library (default  when	 DCMTK
       uses shared libraries).

       The  mapping  table  files  are	expected  in  DCMTK's  <datadir>.  The
       DCMICONVPATH environment	variable can be	used to	 specify  a  different
       location.  If  a	 different location is specified, those	mapping	tables
       also replace any	built-in tables.

FILES
       <datadir>/dsr2xml.xsd - XML Schema file

SEE ALSO
       xml2dsr(1), dcmconv(1)

COPYRIGHT
       Copyright (C) 2000-2024 by OFFIS	e.V., Escherweg	 2,  26121  Oldenburg,
       Germany.

Version	3.6.9			Wed Dec	11 2024			    dsr2xml(1)

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